K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917

Soundararajan, Manonmani; Bünau, Rudolf von; Oelschlaeger, Tobias A.

doi:10.3389/fmicb.2019.02783

Cited by 23 publications

(20 citation statements)

References 95 publications

(106 reference statements)

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“…RcsA has recently been identified as one of the top candidates that increased E . coli fitness in the presence of several phages, including T4 [ 41 – 44 ], by inducing the capsule synthesis gene cluster that triggers the overproduction of colanic acid [ 40 ]. Furthermore, we identified additional mutations likely hitchhiking with the capsule associated SNP, as they were either present after 6 h but not after 24 h exposure to T4, or were present at low frequencies ( S1 Table ).…”

Section: Resultsmentioning

confidence: 99%

“…This fundamental gap, in our knowledge, is partly due to the fact that bacteria–phage interactions have traditionally been investigated via population-level studies that do not permit the dissection of phenotypic heterogeneities within populations. Here, we fill this fundamental gap by demonstrating that in contrast with known genetic resistance mechanisms in well-mixed environments [ 41 , 42 , 59 ], E . coli display 3 previously unrecognised short-term phenotypic resistance strategies to phage T4 in the presence of ephemeral spatial refuges.…”

Section: Discussionmentioning

confidence: 99%

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Individual bacteria in structured environments rely on phenotypic resistance to phage

et al. 2021

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Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria–phage interactions in naturally structured environments.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Individual bacteria in structured environments rely on phenotypic resistance to phage

et al. 2021

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“…By its size, the capsule can hide phage receptors and block phage infection [ 22 ]. Since most Kpn are capsulated, many of its virulent phages evolved to overcome the capsule barrier by encoding serotype-specific depolymerases in their tail proteins [ 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

et al. 2021

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Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the high-priority multidrug-resistant nosocomial pathogens (ESKAPE), the first point of contact between the cell and virions or conjugative pili is the capsule. While the capsule can be a barrier to MGEs, it also evolves rapidly by horizontal gene transfer (HGT). Here, we aim at understanding this apparent contradiction by studying the covariation between the repertoire of capsule genes and MGEs in approximately 4,000 genomes of Klebsiella pneumoniae (Kpn). We show that capsules drive phage-mediated gene flow between closely related serotypes. Such serotype-specific phage predation also explains the frequent inactivation of capsule genes, observed in more than 3% of the genomes. Inactivation is strongly epistatic, recapitulating the capsule biosynthetic pathway. We show that conjugative plasmids are acquired at higher rates in natural isolates lacking a functional capsular locus and confirmed experimentally this result in capsule mutants. This suggests that capsule inactivation by phage pressure facilitates its subsequent reacquisition by conjugation. Accordingly, capsule reacquisition leaves long recombination tracts around the capsular locus. The loss and regain process rewires gene flow toward other lineages whenever it leads to serotype swaps. Such changes happen preferentially between chemically related serotypes, hinting that the fitness of serotype-swapped strains depends on the host genetic background. These results enlighten the bases of trade-offs between the evolution of virulence and multidrug resistance and caution that some alternatives to antibiotics by selecting for capsule inactivation may facilitate the acquisition of antibiotic resistance genes (ARGs).

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“…Effect of polymyxin B on adsorption of phage to LPS. To determine if LPS is the receptor of phage JS09, the adsorption efficiency method was used, adapted from a previous report with modifications (36)(37)(38). One hundred microliters of double-distilled water containing 250 mg/ml PMB was added to 900 ml of WT EK99-F41 cell suspension containing approximately 5 Â 10 8 CFU/ml, and the mixture was incubated at 37°C for 1 h. One sample received 100 ml of double-distilled water as the control.…”

Section: Methodsmentioning

confidence: 99%

A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli

Zhou

Bao

Zhang

et al. 2021

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Our understanding of the mechanisms underlying phage-bacterium interactions remains limited. In Escherichia coli, RapZ regulates glucosamine-6-phosphate (GlcN6P) metabolism, the formation of which initiates synthesis of the bacterial cell envelope, including lipopolysaccharides (LPS). However, the role of RapZ, if any, on phage infectivity remains to be investigated. Here, we isolated strains of enterotoxigenic E. coli (ETEC) resistant to its specific lytic bacteriophage vB_EcoM_JS09 (JS09) in a phage aerosol spray experiment. Whole-genome analysis of phage-resistant bacteria revealed the rapZ gene acquired a premature stop mutation at amino acid 227. Here, we report that the mutation in the rapZ gene confers resistance by inhibiting 93.5% phage adsorption. Furthermore, this mutation changes the morphology of phage plaques, reduces efficiency of plating and phage propagation efficiency, and impairs the infectivity of phage JS09 against ETEC. Using scanning electron microscopy assays, we attribute the inability of the phage to adsorb to the loss of receptors in strains with defective RapZ. Analysis of the LPS profile shows that strains with defective RapZ inhibit phage infection by changing the LPS profile in E. coli. Preincubation of phage JS09 with LPS extracted from a wild-type (WT) strain blocked infection, suggesting LPS is the host receptor for phage JS09 adsorption. Our data uncover the mechanism by which ETEC resists infection of phage JS09 by mutating the rapZ gene and then increasing the expression of glmS and changing the phage receptor-LPS profile. These findings provide insight into the function of the rapZ gene for efficient infection of phage JS09. IMPORTANCE The development of phage-resistant bacteria is a challenging problem for phage therapy. However, our knowledge of phage resistance mechanisms is still limited. RapZ is an RNase adaptor protein encoded by the rapZ gene and plays an important function in Gram-positive and Gram-negative bacteria. Here, we report the whole-genome analysis of a phage-resistant enterotoxigenic Escherichia coli (ETEC) strain, which revealed that the rapZ gene acquired a premature stop mutation (E227Stop). We show that the premature stop mutation of rapZ impairs the infectivity of phage JS09 in ETEC. Furthermore, our findings indicate that ETEC becomes resistant against the adsorption and infection of phage JS09 by mutating the rapZ gene, increasing the expression of glmS, and changing the phage receptor-LPS profile. It is also first reported here that RapZ is essential for efficient infection of phage JS09.

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K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917

Cited by 23 publications

References 95 publications

Individual bacteria in structured environments rely on phenotypic resistance to phage

Individual bacteria in structured environments rely on phenotypic resistance to phage

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli

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